Package com.compomics.util.experiment.biology.aminoacids.impl

Class Z

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.aminoacids.AminoAcid

com.compomics.util.experiment.biology.aminoacids.impl.Z

All Implemented Interfaces:

Serializable

public class Z
extends AminoAcid

Glu or Gln: Glx (Mascot).

Author:

Harald Barsnes

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.aminoacids.AminoAcid

AminoAcid.Property

Field Summary

Fields inherited from class com.compomics.util.experiment.biology.aminoacids.AminoAcid

A, AMINO_ACID_STRINGS, aminoAcidCombinations, B, C, D, E, F, G, H, I, J, K, L, M, monoisotopicAtomChain, N, name, O, P, Q, R, S, singleLetterCode, standardGeneticCode, subAminoAcidsWithCombination, subAminoAcidsWithoutCombination, T, threeLetterCode, U, V, W, X, Y, Z

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
Z()	Constructor.

Method Summary

Modifier and Type	Method	Description
double	getBasicity()	Returns the basicity according to PMID 14730315.
double	getHelicity()	Returns the helicity according to PMID 14730315.
double	getHydrophobicity()	Returns the hydrophobicity according to PMID 14730315.
double	getMonoisotopicMass()	Returns the mass of the amino acid.
double	getPI()	Returns the pI.
double	getPK1()	Returns the pK1.
double	getPK2()	Returns the pK2.
double	getPKa()	Returns the pKa.
int	getVanDerWaalsVolume()	Returns the van der Waals volume in Å3.
boolean	iscombination()	Indicates whether the amino acid object refers to a combination of amino acids like B, J, Z or X.

Methods inherited from class com.compomics.util.experiment.biology.aminoacids.AminoAcid

equals, getAminoAcid, getAminoAcid, getAminoAcidFromGeneticCode, getAminoAcids, getAminoAcidsList, getCombinations, getIndex, getMatchingAminoAcid, getMatchingSequence, getMonoisotopicAtomChain, getNUnique, getProperty, getSingleLetterCodeAsChar, getStandardGeneticCode, getStandardGeneticCodeForCombination, getSubAminoAcids, getSubAminoAcids, getUniqueAminoAcids, getUniqueIndex, isAa, isAa, isUniqueAa

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Z

public Z()

Constructor.

Method Details

getMonoisotopicMass

public double getMonoisotopicMass()

Description copied from class: AminoAcid

Returns the mass of the amino acid.

Overrides:

getMonoisotopicMass in class AminoAcid

Returns:

the mass of the amino acid

iscombination

public boolean iscombination()

Description copied from class: AminoAcid

Indicates whether the amino acid object refers to a combination of amino acids like B, J, Z or X.

Specified by:

iscombination in class AminoAcid

Returns:

an boolean indicating whether the amino acid object refers to a combination of amino acids like B, J, Z or X

getHydrophobicity

public double getHydrophobicity()

Description copied from class: AminoAcid

Returns the hydrophobicity according to PMID 14730315.

Specified by:

getHydrophobicity in class AminoAcid

Returns:

the hydrophobicity

getHelicity

public double getHelicity()

Description copied from class: AminoAcid

Returns the helicity according to PMID 14730315.

Specified by:

getHelicity in class AminoAcid

Returns:

the helicity

getBasicity

public double getBasicity()

Description copied from class: AminoAcid

Returns the basicity according to PMID 14730315.

Specified by:

getBasicity in class AminoAcid

Returns:

the basicity

getPI

public double getPI()

Description copied from class: AminoAcid

Returns the pI.

Specified by:

getPI in class AminoAcid

Returns:

the pI

getPK1

public double getPK1()

Description copied from class: AminoAcid

Returns the pK1.

Specified by:

getPK1 in class AminoAcid

Returns:

the pK1

getPK2

public double getPK2()

Description copied from class: AminoAcid

Returns the pK2.

Specified by:

getPK2 in class AminoAcid

Returns:

the pK2

getPKa

public double getPKa()

Description copied from class: AminoAcid

Returns the pKa. 0.0 if none.

Specified by:

getPKa in class AminoAcid

Returns:

the pKa

getVanDerWaalsVolume

public int getVanDerWaalsVolume()

Description copied from class: AminoAcid

Returns the van der Waals volume in Å3.

Specified by:

getVanDerWaalsVolume in class AminoAcid

Returns:

the van der Waals volume